man/plotVelocityStream.Rd
 229fea0e  % Generated by roxygen2: do not edit by hand % Please edit documentation in R/plotVelocityStream.R \name{plotVelocityStream} \alias{plotVelocityStream} \title{Velocity stream plot in low-dimensional space} \usage{ plotVelocityStream( sce, embedded, use.dimred = 1, color_by = "#444444", color.alpha = 0.2, grid.resolution = 60, scale = TRUE, stream.L = 10, stream.min.L = 0, stream.res = 4, stream.width = 8, color.streamlines = FALSE, color.streamlines.map = c("#440154", "#482576", "#414487", "#35608D", "#2A788E", "#21908C", "#22A884", "#43BF71", "#7AD151", "#BBDF27", "#FDE725"), arrow.angle = 8, arrow.length = 0.8 ) } \arguments{ \item{sce}{A \linkS4class{SingleCellExperiment} object containing low-dimensional coordinates, e.g., after t-SNE, in its \code{\link{reducedDims}}.} \item{embedded}{A low-dimensional projection of the velocity vectors into the embedding of \code{sce}. This should be of the same dimensions as \code{sce} and is typically produced by \code{\link{embedVelocity}}.} \item{use.dimred}{String or integer scalar specifying the reduced dimensions to retrieve from \code{sce}.} \item{color_by}{A character scalar specifying a column in \code{colData(sce)} to color cells in the phase graph. Alternatively, \code{color_by} can be set to a valid R color to be used to color cells.} \item{color.alpha}{An integer scalar giving the transparency of colored cells. Possible values are between 0 (fully transparent) and 1.0 (opaque).} \item{grid.resolution}{Integer scalar specifying the resolution of the grid, in terms of the number of grid intervals along each axis.} \item{scale}{Logical scalar indicating whether the averaged vectors should be scaled by the grid resolution.} \item{stream.L}{Integer scalar giving the typical length of a streamline low-dimensional space units.} \item{stream.min.L}{A numeric scalar with the minimum length of segments to be shown.} \item{stream.res}{Numeric scalar specifying the resolution of estimated streamlines (higher numbers increase smoothness of lines but also the time for computation).} \item{stream.width}{A numeric scalar controlling the width of streamlines.} \item{color.streamlines}{Logical scalar. If \code{TRUE} streamlines will be colored by local velocity. Arrows cannot be shown in that case.} \item{color.streamlines.map}{A character vector specifying the color range used for mapping local velocities to streamline colors. The default is \code{viridisLite::viridis(11)}.} \item{arrow.angle, arrow.length}{Numeric scalars giving the \code{angle} and \code{length} of arrowheads.} } \value{ A \code{ggplot2} object with the streamline plot. } \description{ Plot velocities embedded into low-dimensional space as a stream plot. Stream lines are lines that follow the gradient in the velocity field and illustrate paths that cells could follow based on observed RNA velocities. } \details{ \code{grid.resolution} and \code{scale} are passed to \code{\link{gridVectors}}, which is used to summarized the velocity vectors into an initial grid. A full regular grid is computed from that and used in \code{\link[metR]{geom_streamline}} to calculate streamlines. The following arguments are passed to the arguments given in parenthesis of \code{\link[metR]{geom_streamline}}: \code{stream.L} (\code{L}), \code{stream.res} (\code{res}), \code{stream.min.L} (\code{min.L}), \code{arrow.angle} (\code{arrow.angle}) and \code{arrow.length} (\code{arrow.length}). Streamlines are computed by simple integration with a forward Euler method, and \code{stream.L} and \code{stream.res} are used to compute the number of steps and the time interval between steps for the integration. \code{stream.width} is multiplied with \code{..step..} estimated by \code{\link[metR]{geom_streamline}} to control the width of streamlines. } \examples{ library(scuttle) set.seed(42) sce1 <- mockSCE(ncells = 100, ngenes = 500) sce2 <- mockSCE(ncells = 100, ngenes = 500) datlist <- list(X=counts(sce1), spliced=counts(sce1), unspliced=counts(sce2)) out <- scvelo(datlist, mode = "dynamical") em <- embedVelocity(reducedDim(out, 1), out)[,1:2] plotVelocityStream(out, em) plotVelocityStream(out, em, color.streamlines = TRUE) } \seealso{ \code{\link{gridVectors}} used to summarize velocity vectors into a grid (velocity field), the \pkg{ggplot2} package used for plotting, \code{\link[metR]{geom_streamline}} in package \pkg{metR} used to calculate and add streamlines from the RNA velocity field to the plot, \code{\link[viridisLite]{viridis}} for creation of color palettes. } \author{ Michael Stadler }